I have an image like this:
I need to count number of cells in each cell chain as automatically as possible. For example the image above has one chain of about length 49, but I have also images with more chains.
My current approach is the following:
- Threshold to separate the cell chain from the background. (How do you automatically find a threshold for a specific image?)
- Use Dilate a couple of times and then erode to connect the cells of a chain which are not connected already. (How often?)
- Then I would use something like flood fill to identify chains. (This would be a plugin.)
- Watershed to split a chain into cells resulting in this image:
- Flood fill again to indentify cells and look up the center of each cell in the chain data of step 3.
I also considered Hough Transform, but cells of this size and shape are hardly to identify as a circle.
Any suggestions how to solve this problem in a more elegant and robust way mostly with tools already provided by ImageJ?